Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

Abstract

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

“…Despite the different numbers of SNP (40,958 vs. 43,043) and the different components (PC1 and PC3 vs. PC1 and PC2) used in our study, Fig. 1 shows the same results as those reported by Decker et al (2014) Decker et al (2014), European cattle breeds were exported to Asia and admixed with Asian taurines. Moreover, the Sicilian breeds formed nonoverlapping clusters with other breeds.…”

“…Ancestry models with 4 ancestral populations implemented in Admixture (Fig. 2) provided the same results as those reported by Decker et al (2014) that used an ancestry model with 3 ancestral populations. In fact, the 3 major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed (Fig.…”

“…To understand the genetic relationship within and among breeds, genotypes from 1,543 other animals belonging to 134 domesticated bovid breeds were used (Decker et al, 2013). These breeds arose from 3 domesticated (sub)species: Bos javanicus, B. taurus indicus, and B. t. taurus.…”

“…Inc., Cary, NC) and PLINK (Purcell et al, 2007). Single nucleotide polymorphisms that did not satisfy the following quality criteria were discarded: 1) SNP located on autosomes and common to all breeds, 2) MAF ≥ 0.0005, and 3) SNP with genotyping rate ≥ 0.90 according to Decker et al (2014).…”

Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers

“…The Nguni is considered as a sub-type of Sanga (Bos taurus Africanus) that originated from the imported Arabian Peninsula bulls (Hanotte et al 2000;Decker et al 2014). Mitochondrial DNA analysis confirmed the origin of Nguni cattle from humped Bos indicus and the humpless Bos taurus (Horsburgh et al 2013).…”